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CharonY

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Everything posted by CharonY

  1. There may be something lost in translation, but "testing the DNA binding domain of a protein to a transcription factor" does not really make sense as a transcription factor is generally a protein with DNA binding properties. Thus it would imply a protein-protein interaction. It would help if you clarified what is supposed to bind to what. I will for now assume that you want to test the binding of a protein (or its DNA binding domain) to a cognate DNA region (essentially an EMSA or electrophoretic mobility shift assay). Assuming that to be true I have some issues understanding the image. What is in lane 1? It is labelled as no protein, but what is there? Are the fragments in 2-4 referring to specific fragments of the DNA-binding protein? Or does it refer to a DNA-fragment? On the same note, what precisely is in lane 6-8? Are the fragments referring to DNA now, or to protein fragments? If the fragment are all referring to proteins, where is DNA added? Also what kind of visualization is shown in the gel? I.e. are only the proteins dyed or are DNA and protein visualized? I could start guessing and assuming that the fragments are really referring to DNA stretches, but I would prefer if you could clarify. Note that domain refer to specific regions on a protein and not on DNA..
  2. The problem with this kind of arguments is that it is based on a complete lack of understanding of genetics and argues from there. One cannot really deconstruct individual arguments without pointing out that everything is nonsense and educated from the very basics, which would take more time than most (on either side of the argument) are willing to invest. Nonetheless, a few points to address: - changes in genome size can be quick and dramatic. Common mechanisms are duplications of whole areas and even chromsomes, but also due to mobile genetic elements such as viruses, transposons, plasmids, integrons and so on. These changes may not persist through the generation if they are deleterious, but there are plenty of examples in which they do (just think about polyploidy, i.e. multiplications of chromosomal sets) in plants. The additional genetic material may not even change the phenotype, but they allow for mutations and creations of genetic variants which may not have beem possible with a more restricted genome. This leads me to the topic of mutations. Of course mutations do create novel material. A change in a base can result in a change in an amino acid, which in turn may change the function of a protein. More dramatic changes can be induced by changing the expression pattern (e.g. by mutating regulators or regulatory DNA sequences). There are plenty of examples for that too (again, basic genetics). The summary is basically that evolution has nothing to do with randomly adding base pairs to the mix, nor do the molecular mechanisms work that way, which makes all the toying with numbers (I am hesitant to even call that math) rather pointless.
  3. In case someone is wondering, OP is referring to two ecotypes of Arabidopsis thaliana (Columbia and Landsberg erecta). Both have been sequenced, so you should find the at the respective data repositories from the original sequencing consortia or on the NCBI server. Which one you need depends on whether you want AA or DNA sequences (title refers to gene, post implies protein)...
  4. The amino acid distrubution can vary quite a bit if we look at all organisms (at most one order of magnitude, usually far less). The largest differences are found with extremophiles which require specific adaptions to allow their proteins to function under extreme conditions.
  5. Also chances are that this will be the time where you will have most fun with science (long enough to appreciate some of the finer elements of science, not long enough to be bogged down by other duties). Have fun, but also try to get to know people and stay in touch. You never know what contacts can be good for.
  6. OK, this pretty much all wrong. The major discussed actions of silver particles involve the formation of oxidative stress and inhibitaiton of enzymes due to interaction with thiol groups.
  7. Generally the silver ions are what kill off bacteria, thus the form of silver is relevant. Nanoparticles are, due to their larger surface, more effective, for instance.
  8. Well, I assume they refer to obsessive praying, or the inability not to pray.
  9. The funnel is an elegant way to do it. Parafilm is a really bad idea. If you do not have access to anything, I would take bottle that is sealed tightly before shaking or vortexing phenol. For the most part, a stirring bar works also well, but I would disrupt the strring a little bit every now and then and restart, to ensure homogenous mixing. In the end it should look like a nice emulsion, without any obvious separation. The problem with decanting is that either you will waste quite a bit (if you want to avoid getting the aqueous phase) or you will have to pipette the last bit rather carefully. Certainly not ideal, but doable.
  10. For a career the choice of course will mostly have little to no impact (especially if you do not precisely the job you wan to get into). In addition the actual topics covered under these names are going to vary quite a lot from university to university. IMO the most useful courses are heavy on the analytic side (as they are more universally applicable), but this could be covered by all of these topics. What you learn (and thus, how useful it will be to you) will be much more dependent on the design of the course and the abilities of the teachers, rather than the overall topic.
  11. Education and use of condoms have reduced spread of HIV. From the 80s to the 90s there was a steady decline in new incidences and has more or less remained steady since then (for most of Europe and the US at least). In addition scientific and medical advances helped in the diagnosis and treatment and management (though not cure) of the disease. It is not a novel finding that some youngsters (and others) miscalculate or ignore risks. That is why education can help.
  12. Complacency is unfortunately very common (I am certainly also guilty of it at times). I do have the advantage of having a mix of hazardous and non-hazardous cells (e.g. prokaryotes) and I try to slip into different mindsets for each type of work. Regarding growth in the eyes, I would not think it very likely considering that most cell lines are wimps and require quite some pampering (though you will know more about your particular cell line than I do). Also there would be issues in adherence, considering that there are quite a few mechanisms to get rid of stuff from our eyes. But a check every now and then is certainly not the worst one could do.
  13. I assume you meant the bottom right is interphase and the middle is prophase? Look at the nucleus, do you see any differences?
  14. This can refer to a lot of different things and hence, techniques. Structure can be elucidated by e.g.: -crystallography -NMR -MS -molecular biological techniques Functional analyses often include: -mutagenesis/ knock down -fluorescence based investigations -in vitro analyses and many more (as well as combinations thereof). It really depends on the questions the lab is trying to answer.
  15. I can see no scientific basis for the any of the assertions. The similarities provided in the examples are crude at best and certainly share no structural similarities. Certainly speculations material.
  16. How about a shorter term after election (as evaluation time so to say), followed by a longer one after that?
  17. Everything ajb said. Note that the hard part is AFTER getting the PhD. Neither passion nor degree will guarantee you a career. It is more that once you realized what it entails, without passion there is no good reason to go through all the post-degree madness.
  18. Technically all human cell lines are considered to be potential risks (and hence BSL2), mainly due to presence of viruses. The well-known HeLa carries HPV, for example. However, the actual risk are relatively low. They viruses are generally only found in low concentrations (if at all) and a small droplet is not likely to do much. In fact, if you work long enough with them and are not careful there is a big chance that you inhaled more during pipetting (when not working under a biosafety bench), centrifugation, or other aerosol-generated processes (which you should not, but with many people working in a lab you never know). Lab safety is all about preparing for the worst, and it is good that you are aware of potential risks. But again, the likelihood of immediate consequences thereof are minuscule. You should report the event, however, to have it documented regardless.
  19. Without looking at those and reference chromatograms (values are too arbitrary to be looked at without reference points) and a look on reproducibility one cannot say too much about it. The peaks could e.g. be contaminations, especially if they show up at the same time. But again, not enough info to troubleshoot.
  20. I have issues with that. It assumes there is some kind of homeostasis within our body and/or cells. However, aging is progressive (think of cell maturation, for example). There is no phase that I could think of where there is a homeostatic condition resulting in "normal gene expression" (I also have no clue what that is) and hence, no aging (for a while, at least). This simply does not agree what we know about cell development and aging, for example (i.e. progressive mitochondrial damage; telomere length and telomerase activity, etc.). With an erroneous premise, further deliberations are not likely to be accurate.
  21. A classic setup was three oil baths and an undergrad.
  22. Indeed. Although I do think that they may actually have physiological consequences of sorts. For example, such stretches may affect DNA dynamics and in a subtle way alter gene expression strengths. Although this is more likely of relevance for single-celled organisms and the evolutionary consequences are likely to be of more relevance.
  23. Well, the question is what the physiological consequences of these are. Large genomes offer an enormous "habitat" for mobile genetic elements (or, one could argue that they became so large because of them). As the size and structure are somewhat less under selective pressure than in bacteria they may offer quite a different landscape for evolutionary changes. Early analyses of the human genome estimated something close to 45% of the human genome consist of transposable elements (and much higher levels were found in plants). However, their mechanism of replication is quite specific and chances are that an alien virus would not be able to do much.
  24. 1. Only the first methionine is recognized as starting codon (in bacteria, formyl-metionine is actually incorporated at the onset of translation). Further AUG are treated (for the most part) as regular methionine. A simplified way to visualize this is that the ribosome is formed at the ribosome binding area of the mRNA, the mRNA is then pulled through until the start codon is recognized. From there the elongation of the protein is processed normally, until it is terminated. In some cases (mostly viral genomes) genes can be stacked. In this cases a second ribosome binding site can be found within a larger coding area so that the initiations starts further downstream. 2. The implications can be quite deep. To understand some of them, one has to know that the genetic code is realized by the presence of tRNA that carry a specific aa with a respective anticodon, which recognizes the particular sequence on the mRNA. So mechanistically each codon requires the presence of their respective tRNA. I.e. a tRNA carrying the respective anticodon, coupled with a given amino acid (phenylalanine in this case). Some implications: - protein synthesis can be controlled by tRNA levels. One particular tRNA may be present in low concentrations, for whatever reasons, and genes carrying their codons may not become (fully) translated. - mutations within each codon can result in different amino acids (not so much an issue in this example), likewise, mutations in the genes coding for the respective tRNAs will result in different effects (as these are different genes) - on a similar note, different bases (uracil vs cytosine in this example) have different propensity to mutate in presence of different agents, so mutation rates may differ
  25. Yes, something else is likely to be needed, but not necessarily of viral origin. I was thinking if intracellular parasites in general. Bacteria are an interesting example (think in terms of mitochondrial-nuclear gene transfer). The precise mechanisms are afaik unknown, however.
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